Module pipeline 

QSM pipeline stages and utilities

Shared stage functions that both qsmxt.rs and qsmbly call to ensure identical processing. Each consumer calls the stages individually with its own I/O and caching layer on top.

Pipeline stages (typical order)

1. run_field_mapping — multi-echo phase → B0 field map (ppm)
2. run_bg_removal — total field → local field (ppm)
3. run_dipole_inversion — local field → susceptibility (ppm)
4. apply_reference — mean subtraction

For TGV, use run_tgv which combines steps 1-4 internally.

Combined algorithms

• HARPERELLA: SMV-based exterior Laplacian estimation (Li et al., 2014)
• iHARPERELLA: Phase-domain exterior estimation with improved low-freq suppression (Li et al., 2015)

Re-exports

pub use phase_utils::scale_phase_to_pi;

pub use phase_utils::hz_to_ppm;

pub use phase_utils::rads_to_ppm;

pub use phase_utils::rss_combine;

pub use phase_utils::erode_mask;

pub use phase_utils::dilate_mask;

pub use referencing::apply_reference;

pub use masking::apply_mask_ops;

pub use masking::build_mask_section;

pub use masking::run_masking;

pub use field_mapping::run_field_mapping;

pub use bg_removal::run_bg_removal;

pub use inversion::run_dipole_inversion;

pub use inversion::run_tgv;

pub use inversion::run_nextqsm;

pub use inversion::run_iqsm;

pub use inversion::run_iqsm_plus;

pub use inversion::run_iqfm;

pub use separation::run_separation;

pub use separation::SeparationInputs;

pub use separation::SeparationResult;

pub use qsmart::run_qsmart;

pub use config::*;

Modules

bg_removal

Background field removal stage

config

Pipeline configuration types

field_mapping

Field mapping stage

inversion

Dipole inversion stage

masking

Masking stage

phase_utils

Phase and field conversion utilities

qsmart

QSMART two-stage reconstruction

referencing

QSM referencing

separation

Susceptibility source-separation stage.